Contacts of the strand formed by residues 478 - 482 (chain G) in PDB entry 5CAY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 478 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361G LEU* 4.9 4.7 - - + -
367G TYR 5.7 0.4 + - - -
370G THR* 3.6 23.8 - - + +
371G ASN* 5.3 0.2 + - - -
375G LYS 3.9 1.5 + - - +
376G ILE* 3.2 37.8 - - + -
377G ARG* 3.5 15.6 + - - -
470G ILE* 3.9 9.1 - - + +
471G ASP 2.8 22.1 + - - -
472G GLY* 3.1 10.1 + - - -
473G GLY 3.5 15.7 + - - +
477G GLN* 1.3 80.8 + - - +
479G ASN* 1.3 69.6 + - - +
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Residues in contact with ASN 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377G ARG* 3.3 38.6 + - - +
379G ILE* 3.3 28.8 - - + +
469G ASN 3.8 1.2 - - - +
471G ASP* 3.1 38.7 + - + +
477G GLN 4.3 6.8 + - - -
478G THR* 1.3 84.7 + - - +
480G ILE* 1.3 64.3 + - - +
481G THR* 3.9 9.7 + - + +
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Residues in contact with ILE 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G ILE* 5.3 4.0 - - + -
357G VAL* 5.0 8.3 - - + -
358G LYS* 4.9 6.7 - - + -
361G LEU* 3.5 21.3 - - + -
376G ILE* 3.9 15.3 - - + -
377G ARG 3.0 12.3 + - - +
378G PHE* 3.2 52.5 - - + -
379G ILE* 3.1 18.3 + - - -
468G ALA* 4.7 7.0 - - + -
469G ASN 3.6 4.3 - - - +
470G ILE* 3.3 33.0 - - + -
479G ASN* 1.3 74.4 - - - +
481G THR* 1.3 64.4 + - - +
482G PHE 4.0 0.5 + - - -
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Residues in contact with THR 481 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN* 5.8 1.4 + - - -
379G ILE* 3.1 37.0 - - + -
380G ALA 4.7 5.2 - - - +
381G PRO* 5.1 4.0 - - + -
468G ALA* 3.3 3.5 - - - -
469G ASN* 3.1 39.1 + - - +
471G ASP* 4.9 11.8 + - - +
479G ASN* 3.9 10.5 - - + -
480G ILE* 1.3 72.6 - - - +
482G PHE* 1.3 68.8 + - - +
483G SER* 4.6 0.3 - - - -
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Residues in contact with PHE 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN* 4.5 4.7 + - - -
274G TRP* 3.3 63.0 - + + -
275G PHE* 3.8 31.9 - + - -
354G MET* 5.5 2.9 - - - -
378G PHE* 3.4 42.8 - + + -
379G ILE 3.1 20.2 + - - +
381G PRO* 4.1 20.5 - - + +
408G PHE* 5.5 4.9 - + - -
409G LEU* 4.0 9.9 - - + -
466G ILE* 3.4 31.4 - - + -
467G ILE 3.5 4.0 - - - -
468G ALA* 4.4 0.9 - - + +
481G THR* 1.3 78.9 + - - +
483G SER* 1.3 59.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il